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'''Marker Grid for Fast-LMM Empirical Kinship'''
'''Marker Grid for Fast-LMM Empirical Kinship'''
If you plan to use the Fast-LMM mixed model capability in Rare-Metal-Worker, it is likely preferable that you construct your kinship matrix either 1) with genome-wide markers from a GWAS panel (or 2nd generation exome chip) or 2) a subset of selected markers from the exome chip array. A list of markers can be obtained from Scott. There are many common markers on the first version of the exome chip, and many were selected for fine mapping (of MHC) or because of prior GWAS signals. These markers would ideally be excluded from the set of markers used to construct the empirical kinship matrix.
If you plan to use the Fast-LMM mixed model capability in Rare-Metal-Worker, it is likely preferable that you construct your kinship matrix either 1) with genome-wide markers from a GWAS panel (or 2nd generation exome chip) or 2) a subset of selected markers from the exome chip array. A list of markers can be obtained from Scott. There are many common markers on the first version of the exome chip, and many were selected for fine mapping (of MHC) or because of prior GWAS signals. These latter markers would ideally be excluded from the set of markers used to construct the empirical kinship matrix.
'''Running Times'''
'''Running Times'''
